An improved protein decoy set for testing energy functions for protein structure prediction
Abstract
We have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on sidechains and minimizing clashes. The new set consists of 1,400 model structures for 78 different and diverse protein targets and provides a challenging set for the testing and evaluation of scoring functions. We evaluated the extent to which a variety of all‐atom energy functions could identify the native and close‐to‐native structures in the new decoy sets. Of various implicit solvent models, we found that a solvent‐accessible surface area–based solvation provided the best enrichment and discrimination of close‐to‐native decoys. The combination of this solvation treatment with Lennard Jones terms and the original Rosetta energy provided better enrichment and discrimination than any of the individual terms. The results also highlight the differences in accuracy of NMR and X‐ray crystal structures: a large energy gap was observed between native and non‐native conformations for X‐ray structures but not for NMR structures. Proteins 2003. © 2003 Wiley‐Liss, Inc.
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A second more fundamental problem appears to be the rugged nature of the refinement landscape, with local energy barriers preventing convergence to high accuracy, at least using realizable amounts of computer time.
“A second more fundamental problem appears to be the rugged nature of the refinement landscape, with local energy barriers preventing convergence to high accuracy, at least using realizable amounts of computer time (identifying the global minimum with current scoring functions does not seem to be an issue29).”
From Critical assessment of methods of protein structure prediction (CASP)—Round <scp>XIV</scp> (2021) · cites this paper as [29]
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- Authors
- Tsai, J., Bonneau, R., Morozov, A. V., Kuhlman, B., Rohl, C. A., & Baker, D.
- Affiliations
- Texas A&M University (US)
- Institute for Systems Biology (US)
- University of Washington (US)
- University of California, Santa Cruz (US)
- Corresponding author
- Tsai, Jerry
- Venue
- Proteins: Structure, Function, and Bioinformatics
- Publisher
- Wiley
- Published
- 2003-08-05
- Volume
- 53
- Issue
- 1
- Pages
- 76-87
- ISSN
- 0887-3585 (ISSN-L)
- 1097-0134
- OpenAlex
- W2131169717
- Cited by
- 158
- References
- 34
- Citations by year
- 2025: 2 · 2022: 1 · 2021: 1 · 2020: 5 · 2019: 6 · 2018: 3 · 2017: 9 · 2016: 8 · 2015: 7 · 2014: 10 · 2013: 7 · 2012: 6
- FWCI
- 3.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Proteins Structure Function and Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Serbian Academy of Sciences and Arts
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- protein structure prediction, scoring functions, implicit solvent, NMR structure, X-ray crystal structure
- MeSH terms
- Algorithms, Hydrogen Bonding, Protein Conformation, Proteins, Solvents
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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